ok, I think that's a different problem. I seem to remember some people having a similar problem with the theme windows losing their "on-top ability" after quitting a full-screen app like games. I think the solution was to set up a script (which was run by a bang shortcut) that would hide all the modules before beginning a full-screen app, then another one to un-hide them after you're done. nanostep probably doesn't have functionality like that built in, so you'll have to do it yourself. there are a few posts on hiding modules in the forum, just search for them. however, in case I'm wrong, and this is just an issue with the desktop area being set wrong, then here's what you need to do. the four lines should be set to something like either:
"setdesktoparea #,#,#,##"
or
"SDATop 24
SDABottom -3
SDALeft 3
SDARight -3"
or something similar. the commands all depends on which module is being used by the theme, and since I can't find nanostep, I can't look to see.